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In general we have disabled the option to disable the primary domain check to avoid duplicate content issues as the option itself says.
Now it occurred that we got one sub-blog where we had the need to disable it (because of a combination of translation and linking needs). Naturally we did not like the thought of disabling it for our whole MultiSite-environment. Thus we came up with a small patch to only activate the option on a per blog basis.
Just in case this might come handy to anyone else we wanted to share it: http://pastebin.com/N8YYpzbB
The Patch is based on the latest version (0.5.5.1).
Cheers,
Merl